Contacts of the helix formed by residues 56 - 70 (chain H) in PDB entry 2PGW
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with ASP 56 (chain H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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62C ALA* 4.0 16.0 - - - +
63C ILE* 3.9 20.0 - - + -
66C ARG* 3.0 37.5 + - - +
53H VAL 3.1 5.5 + - - -
55H PRO* 1.3 83.6 - - - +
57H GLN* 1.3 62.8 + - - +
58H THR* 3.5 12.0 + - - -
59H GLY* 2.8 24.3 + - - -
60H THR* 2.8 31.9 + - - +
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Residues in contact with GLN 57 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66C ARG* 4.4 4.2 - - - +
13H PRO* 3.7 1.0 - - + +
14H LEU 3.0 29.5 + - - +
15H VAL* 3.8 7.4 - - - +
33H ALA* 3.6 16.5 - - + +
34H VAL 3.1 11.9 + - - +
35H ASN* 3.1 26.3 - - - +
53H VAL* 3.4 27.2 + - + +
56H ASP* 1.3 73.4 + - - +
58H THR* 1.3 58.5 + - - +
60H THR* 3.3 1.0 + - - -
61H ALA* 2.9 31.7 + - - +
372H TYR* 3.4 29.8 - - + -
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Residues in contact with THR 58 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62C ALA* 5.5 5.8 - - + -
56H ASP* 3.3 11.7 + - - +
57H GLN* 1.3 78.8 - - - +
59H GLY* 1.3 63.2 + - - +
61H ALA* 3.6 4.4 - - - +
62H ALA* 3.2 21.1 + - - +
372H TYR* 2.7 32.3 + - - +
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Residues in contact with GLY 59 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59C GLY* 3.7 27.4 - - - -
62C ALA* 4.4 4.2 - - - +
63C ILE* 4.7 1.8 - - - -
56H ASP* 2.8 21.7 + - - -
58H THR* 1.3 78.5 - - - +
60H THR* 1.3 61.1 + - - +
62H ALA* 3.3 6.2 + - - +
63H ILE* 3.2 28.1 + - - +
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Residues in contact with THR 60 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63C ILE* 4.5 7.4 - - + -
35H ASN* 3.3 10.8 + - - -
52H THR 4.8 1.8 - - - -
53H VAL* 3.0 31.9 + - - +
54H ALA 3.5 16.6 - - - +
55H PRO* 4.2 8.3 - - + -
56H ASP 2.8 20.8 + - - +
57H GLN 3.3 5.5 + - - -
59H GLY* 1.3 70.0 - - - -
61H ALA* 1.3 61.4 + - - +
62H ALA 3.3 0.2 - - - -
63H ILE* 3.3 12.3 + - + +
64H LEU* 2.9 29.6 + - - +
104H GLN* 4.6 2.7 - - - +
105H ILE* 4.1 16.3 - - + +
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Residues in contact with ALA 61 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11H VAL* 4.0 9.7 - - + +
13H PRO* 4.0 20.4 - - + -
35H ASN* 3.4 19.7 - - - +
57H GLN 2.9 20.4 + - - +
58H THR* 3.6 7.0 - - - +
60H THR* 1.3 74.6 + - - +
62H ALA* 1.3 61.5 + - - +
64H LEU* 3.3 4.9 + - - +
65H TYR* 2.9 30.9 + - - +
372H TYR* 5.4 0.4 - - - +
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Residues in contact with ALA 62 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56C ASP* 3.9 19.2 - - - +
58C THR* 5.5 5.4 - - + -
59C GLY* 4.5 6.3 - - - +
58H THR* 3.2 10.9 + - + +
59H GLY 3.5 9.9 - - - +
61H ALA* 1.3 80.0 - - - +
63H ILE* 1.3 56.3 + - - +
65H TYR* 3.4 7.4 + - - +
66H ARG* 3.0 29.6 + - - +
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Residues in contact with ILE 63 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55C PRO* 3.5 35.0 - - + -
56C ASP* 4.0 20.0 - - + -
59C GLY* 4.6 3.4 - - - -
60C THR* 4.7 9.0 - - + -
63C ILE* 4.7 15.0 - - + -
59H GLY 3.2 16.7 + - - +
60H THR* 3.6 16.2 - - + +
61H ALA 3.2 0.2 - - - -
62H ALA* 1.3 74.9 - - - +
64H LEU* 1.3 65.1 + - - +
66H ARG* 3.2 7.0 + - - +
67H LEU* 3.0 28.5 + - + +
91H TYR* 3.8 11.9 - - - +
105H ILE* 4.1 15.3 - - + -
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Residues in contact with LEU 64 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11H VAL* 3.8 21.8 - - + -
35H ASN* 3.7 38.8 - - + +
36H LEU 4.1 3.4 - - - +
37H ILE* 4.1 15.5 - - + -
51H CYS* 3.9 18.8 - - + -
60H THR 2.9 17.7 + - - +
61H ALA 3.6 3.6 - - - +
63H ILE* 1.3 77.8 - - - +
65H TYR* 1.3 62.1 + - - +
67H LEU* 3.4 1.2 + - - +
68H ALA* 3.0 26.3 + - - +
105H ILE* 3.6 29.2 - - + -
109H ILE* 4.0 19.5 - - + -
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Residues in contact with TYR 65 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9H VAL* 3.9 25.2 + - + -
10H ARG* 5.0 2.2 - - - -
11H VAL* 3.6 27.3 - - + +
61H ALA 2.9 17.2 + - - +
62H ALA* 3.7 7.0 - - - +
64H LEU* 1.3 77.5 - - - +
66H ARG* 1.3 64.4 + - + +
68H ALA* 3.3 2.3 + - - -
69H LYS* 3.0 68.2 + - + +
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Residues in contact with ARG 66 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55C PRO* 3.1 26.1 + - - -
56C ASP* 3.1 31.7 + - - +
57C GLN* 4.5 3.0 - - - +
376C ARG* 6.1 0.2 - - - +
62H ALA 3.0 17.5 + - - +
63H ILE* 3.6 6.1 - - - +
65H TYR* 1.3 81.6 - - + +
67H LEU* 1.3 65.8 + - + +
69H LYS* 3.7 13.6 + - - +
70H HIS* 3.2 14.4 + - - -
90H GLU* 2.8 38.9 + - - +
94H HIS* 5.4 5.3 + - - -
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Residues in contact with LEU 67 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55C PRO* 4.6 6.7 - - + -
63H ILE* 3.0 21.2 + - + +
64H LEU 3.9 3.4 - - - +
66H ARG* 1.3 79.7 - - + +
68H ALA* 1.3 62.2 + - - +
70H HIS* 3.2 25.4 + - - +
86H ILE* 3.6 29.3 - - + +
90H GLU* 3.8 26.5 - - + -
91H TYR* 3.7 24.0 - - + +
105H ILE* 3.6 25.4 - - + -
106H PHE* 3.7 24.5 - - + -
109H ILE* 4.0 10.8 - - + -
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Residues in contact with ALA 68 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9H VAL* 3.6 19.7 - - + +
37H ILE* 3.6 29.2 - - + -
64H LEU 3.0 17.7 + - - +
65H TYR* 3.3 4.9 + - - +
67H LEU* 1.3 71.9 - - - +
69H LYS* 1.3 59.2 + - - +
70H HIS 3.0 2.9 - - - -
71H LEU* 2.8 41.3 + - + +
109H ILE* 4.1 9.8 - - + +
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Residues in contact with LYS 69 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9H VAL* 4.0 11.7 - - + +
65H TYR* 3.0 67.4 + - + +
66H ARG* 3.9 9.6 - - - +
67H LEU 3.3 0.8 - - - -
68H ALA* 1.3 76.4 - - - +
70H HIS* 1.3 60.6 + - + +
71H LEU 3.0 1.3 + - - -
72H VAL* 3.2 26.8 + - + +
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Residues in contact with HIS 70 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66H ARG* 3.2 24.1 + - - +
67H LEU* 3.3 14.6 - - - +
68H ALA 3.0 0.8 - - - -
69H LYS* 1.3 77.2 - - - +
71H LEU* 1.3 58.4 + - - +
72H VAL 3.3 1.8 + - - +
74H HIS* 3.0 25.3 + - - -
82H LEU* 5.0 0.4 - - - +
85H ARG* 3.9 16.7 + - - +
86H ILE* 3.7 34.8 - - + -
89H GLN* 3.4 30.8 + - - -
90H GLU* 2.7 28.5 + - + +
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il